User: keegan

gravatar for keegan
keegan50
Reputation:
50
Status:
Trusted
Location:
Last seen:
4 months, 2 weeks ago
Joined:
2 years, 3 months ago
Email:
k*****@jimmy.harvard.edu

Posts by keegan

<prev • 13 results • page 1 of 2 • next >
0
votes
1
answer
172
views
1
answers
Comment: C: dmrseq installation failed
... Looks like this issue has now been resolved and bumphunter is passing build in Bioconductor 3.8. ...
written 4 months ago by keegan50
0
votes
2
answers
250
views
2
answers
Answer: A: Internal bug of DMR-Seq?
... Hi Deepak, Thanks for sending the files. I was able to track down the issue and make a fix. The problem was related to improper handling of very small chromosomes that end up with zero coverage after filtering loci. After applying the fix, the latest version of dmrseq runs your code without errors ...
written 4 months ago by keegan50
0
votes
2
answers
250
views
2
answers
Comment: C: Internal bug of DMR-Seq?
... Thanks for checking on that. I'm not sure where this error is coming from. Would it be possible to send me a small test .rds file that contains the BSseq input object - could just contain the offending chromosome GL4563591 - along with the code used to call dmrseq? If I can reproduce the problem, it ...
written 4 months ago by keegan50
0
votes
2
answers
250
views
2
answers
Comment: C: Internal bug of DMR-Seq?
... Can you inspect the output of BiocManager::valid() ? If it indicates that any packages are out of date, please try updating them and trying again. ...
written 4 months ago by keegan50
2
votes
2
answers
250
views
2
answers
Answer: A: Internal bug of DMR-Seq?
... I think I found the most likely cause of the error being thrown. Essentially, I don't think the error handling for region-level model fitting was correct when the covariate of interest is a multi-level factor. When a region fit failed to converge, it would output a row to the results table that assu ...
written 5 months ago by keegan50
1
vote
2
answers
250
views
2
answers
Comment: C: Internal bug of DMR-Seq?
... Increasing the number of permutations could potentially improve the power of detection, especially if you are currently using very few. You might also check the individual comparisons between normal and each type of pre-cancer separately. In addition, from the code you sent it looks like you are sea ...
written 5 months ago by keegan50
0
votes
2
answers
250
views
2
answers
Comment: C: Internal bug of DMR-Seq?
... Thanks for the additional information. BiocManager is a new package that helps with installation and keeping packages up-to-date - the valid() function checks for out of date packages and outputs instructions to update packages, and the install() function will soon replace biocLite() for installing ...
written 5 months ago by keegan50
0
votes
2
answers
250
views
2
answers
Comment: C: Internal bug of DMR-Seq?
... Hi, Thanks for the report. So that I can reproduce the error, would you be able to give me a bit more information? Specifically, What is the output of BiocManager::valid() on your system? What is the code you are using that produces this error? Likewise, what settings do not produce the error? If ...
written 5 months ago by keegan50
0
votes
1
answer
148
views
1
answers
Comment: C: DMRseq smoothed values
... Ah, yes the smoothed lines generated in plotDMRs() for visualization purposes are generated on the fly, so they are not created for the entire genome. BSmooth() will compute smoothed values for the whole BSseq object, however. Hope that helps! ...
written 7 months ago by keegan50
0
votes
1
answer
148
views
1
answers
Answer: A: DMRseq smoothed values
... Hi swebb1, dmrseq does not compute smoothed methylation values. Instead, it smooths methylation differences with respect to the covariate of interest. These smoothed methylation differences are not stored. If obtaining these values would be useful, I would consider adding an option to store/export ...
written 7 months ago by keegan50

Latest awards to keegan

Scholar 7 months ago, created an answer that has been accepted. For A: dmrseq: cannot adjust for a covariate
Scholar 2.1 years ago, created an answer that has been accepted. For A: dmrseq: cannot adjust for a covariate

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 229 users visited in the last hour